[srividya22]

Hello,

I am using ur script SOLiD2Std.pl to convert 1100 genomes data to base space (fastq)

The script doesnt convert characters after a dot.

I want to convert it to fastq format and align it using Stampy.

Do anyone have a script that can do the conversion properly now ?

[gringer]

I am using ur script SOLiD2Std.pl to convert 1100 genomes data to base space (fastq)

The script doesnt convert characters after a dot.

I want to convert it to fastq format and align it using Stampy.

Do anyone have a script that can do the conversion properly now ?

After a dot, you can't assume anything about the sequence. All subsequent reads should be N in base space. Alignment should always be done in colour-space to get the most information (and least error) from the colour-space sequence.

[BENM]

Hello,

I am using ur script SOLiD2Std.pl to convert 1100 genomes data to base space (fastq)

The script doesnt convert characters after a dot.

I want to convert it to fastq format and align it using Stampy.

Do anyone have a script that can do the conversion properly now ?

I have already fixed some bugs of it, you can try it again.

[srividya22]

downloading SOLid2Std.pl file

Hello BENM,

Where can I get the recent SOLid2Std.pl. because when I googled it I could nt locate it. Can u please specify the path ?

[vz33]

Hi, pliang

Because samt's question is "Convert SOLiD fastq to Illumina fastq", Illumina FASTQ is different from Standard(Sanger) FASTQ in quality format.

The syntax of Solexa/Illumina read format is almost identical to the FASTQ format, but the qualities are scaled differently. Given a character $sq, the following Perl code gives the Phred quality $Q:

$Q = 10 * log(1 + 10 ** (ord($sq) - 64) / 10.0)) / log(10);

The ASCII charactars in Solexa FASTQ means:

CHAR	DEC	QUALITY
A	65	1
B	66	2
C	67	3
D	68	4
E	69	5
F	70	6
G	71	7
H	72	8
I	73	9
J	74	10
K	75	11
L	76	12
M	77	13
N	78	14
O	79	15
P	80	16
Q	81	17
R	82	18
S	83	19
T	84	20
U	85	21
V	86	22
W	87	23
X	88	24
Y	89	25
Z	90	26
[	91	27
\	92	28
]	93	29
^	94	30
_	95	31
`	96	32
a	97	33
b	98	34
c	99	35
d	100	36
e	101	37
f	102	38
g	103	39
h	104	40
;	59	-5
<	60	-4
=	61	-3
>	62	-2
?	63	-1
@	64	0

In contrast to Solexa FASTQ quality, the ASCII characters in standard (sanger) FASTQ, it used to denote:

CHAR	DEC	QUALITY
!       0       -64
!       1       -63
!       2       -62
!       3       -61
!       4       -60
!       5       -59
!       6       -58
!       7       -57
!       8       -56
!       9       -55
!       10      -54
!       11      -53
!       12      -52
!       13      -51
!       14      -50
!       15      -49
!       16      -48
!       17      -47
!       18      -46
!       19      -45
!       20      -44
!       21      -43
!       22      -42
!       23      -41
!       24      -40
!       25      -39
!       26      -38
!       27      -37
!       28      -36
!       29      -35
!       30      -34
!       31      -33
!       32      -32
!       33      -31
!       34      -30
!       35      -29
!       36      -28
!       37      -27
!       38      -26
!       39      -25
!       40      -24
!       41      -23
!       42      -22
!       43      -21
!       44      -20
!       45      -19
!       46      -18
!       47      -17
!       48      -16
!       49      -15
!       50      -14
!       51      -13
!       52      -12
!       53      -11
!       54      -10
"       55      -9
"       56      -8
"       57      -7
"       58      -6
"       59      -5
"       60      -4
#       61      -3
#       62      -2
$       63      -1
$       64      0
%       65      1
%       66      2
&       67      3
&       68      4
'       69      5
(       70      6
)       71      7
*       72      8
+       73      9
+       74      10
,       75      11
-       76      12
.       77      13
/       78      14
0       79      15
1       80      16
2       81      17
3       82      18
4       83      19
5       84      20
6       85      21
7       86      22
8       87      23
9       88      24
:       89      25
;       90      26
<       91      27
=       92      28
>       93      29
?       94      30
@       95      31
A       96      32
B       97      33
C       98      34
D       99      35
E       100     36
F       101     37
G       102     38
H       103     39
I       104     40
J       105     41
K       106     42
L       107     43
M       108     44
N       109     45
O       110     46
P       111     47
Q       112     48
R       113     49
S       114     50
T       115     51
U       116     52
V       117     53
W       118     54
X       119     55
Y       120     56
Z       121     57
[       122     58
\       123     59
]       124     60
^       125     61
_       126     62
`       127     63
a       128     64

So it is easy to conver Solexa->Sanger quality, you just need to build a conversion table in PERL script, just like this:
# Solexa->Sanger quality conversion table
my @conv_table;
for (-64..64) {
$conv_table[$_+64] = chr(int(33 + 10*log(1+10**($_/10.0))/log(10)+.499));
}

I am trying to write a universal script for Solexa/Illumina, SOLiD/ABi, 454/Roche, 3730/Sanger,...transforming to each other format for different purpose, but I need to know your requirements, after that, I will share it to you all.

Hope I answer your question.
BTW I attach the SOLiD2std.pl for your question, just make a little change in SOLiD2Solexa.pl

which format fastq file does the bowtie2 use ? standard fastq or Solexa FASTQ? Thank you!